The Windows Azure Tomcat Solution is designed in a way that you can update your Tomcat project outside VS2010 project.
The VS2010 application will be deployed once however whenever you would need to update, Tomcat, Java Run time or your own Tomcat based solution, you can update without updating your Windows Azure application.
This project is based on Startup task in which Tomcat, Java and your project is downloaded from Azure Storage and then installed in Azure VM.
Full source code is available for startup task and solution via : http://tomcatazure.codeplex.com/
For a more details and complete setup guides look here